#!/bin/bash

cd /data/cellrangerdata/200423
${ID}=200423_run1

/home/ssm-user/cellranger/cellranger-3.1.0/cellranger aggr \
--id=200423_run1 \
--csv=/data/cellrangerdata/200423/aggregation.csv \
--normalize=none \		#mapped or none - read depth downsampling or nothingf niets
--nosecondary &

rm -rf /data/cellrangerdata/${ID}/SC_RNA_AGGREGATOR_CS 	#tijdelijke bestanden van cellranger weer verwijderen

